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Persistent homology

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https://www.readbyqxmd.com/read/28229982/circulating-free-dna-mutation-associated-with-response-of-targeted-therapy-in-human-epidermal-growth-factor-receptor-2-positive-metastatic-breast-cancer
#1
Qing Ye, Fan Qi, Li Bian, Shao-Hua Zhang, Tao Wang, Ze-Fei Jiang
BACKGROUND: The addition of anti-human epidermal growth factor receptor 2 (HER2)-targeted drugs, such as trastuzumab, lapatinib, and trastuzumab emtansine (T-DM1), to chemotherapy significantly improved prognosis of HER2-positive breast cancer patients. However, it was confused that metastatic patients vary in the response of targeted drug. Therefore, methods of accurately predicting drug response were really needed. To overcome the spatial and temporal limitations of biopsies, we aimed to develop a more sensitive and less invasive method of detecting mutations associated with anti-HER2 therapeutic response through circulating-free DNA (cfDNA)...
2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28214649/evaluation-of-dioxins-and-dioxin-like-compounds-from-a-cement-plant-using-carbide-slag-from-chlor-alkali-industry-as-the-major-raw-material
#2
Yuyang Zhao, Jiayu Zhan, Guorui Liu, Minghui Zheng, Rong Jin, Lili Yang, Liwei Hao, Xiaolin Wu, Xian Zhang, Pu Wang
Carbide slag produced from chlor-alkali industry contains high amounts of calcium compounds and can potentially be used as raw material for cement production; however, it contains large amounts of chlorine so it is essential to evaluate the emissions of chlorinated organic pollutants, including polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), polychlorinated biphenyls (PCBs), and polychlorinated naphthalenes (PCNs). A field study of the emission profiles of these pollutants in a cement plant using such slag was performed...
February 14, 2017: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/28208329/persistent-homology-analysis-of-craze-formation
#3
Takashi Ichinomiya, Ippei Obayashi, Yasuaki Hiraoka
We apply a persistent homology analysis to investigate the behavior of nanovoids during the crazing process of glassy polymers. We carry out a coarse-grained molecular dynamics simulation of the uniaxial deformation of an amorphous polymer and analyze the results with persistent homology. Persistent homology reveals the void coalescence during craze formation, and the results suggest that the yielding process is regarded as the percolation of nanovoids created by deformation.
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28192542/functional-diversity-of-secreted-cestode-kunitz-proteins-inhibition-of-serine-peptidases-and-blockade-of-cation-channels
#4
Martín Fló, Mariana Margenat, Leonardo Pellizza, Martín Graña, Rosario Durán, Adriana Báez, Emilio Salceda, Enrique Soto, Beatriz Alvarez, Cecilia Fernández
We previously reported a multigene family of monodomain Kunitz proteins from Echinococcus granulosus (EgKU-1-EgKU-8), and provided evidence that some EgKUs are secreted by larval worms to the host interface. In addition, functional studies and homology modeling suggested that, similar to monodomain Kunitz families present in animal venoms, the E. granulosus family could include peptidase inhibitors as well as channel blockers. Using enzyme kinetics and whole-cell patch-clamp, we now demonstrate that the EgKUs are indeed functionally diverse...
February 13, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28192223/emergence-of-multi-drug-resistance-among-soil-bacteria-exposing-to-insecticides
#5
Kirubakaran Rangasamy, Murugan Athiappan, Natarajan Devarajan, Javid A Parray
Impacts of pesticide exposure on the soil microbial flora and cross resistance to antibiotics have not been well documented. Development of antibiotic resistance is a common issue among soil bacteria which are exposing to pesticides continuously at sub-lethal concentration. The present study was focused to evaluate the correlation between pesticide exposures and evolution of multi drug resistance among isolates collected from soil applied with insecticides. Twenty five insecticide (Monochrotophos) degrading bacteria were isolated from contaminated agricultural soil...
February 9, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28184004/ets-proto-oncogene-1-transcriptionally-up-regulates-the-cholangiocyte-senescence-associated-protein-cyclin-dependent-kinase-inhibitor-2a
#6
Steven P O'Hara, Patrick L Splinter, Christy E Trussoni, Maria J Lorenzo Pisarello, Lorena Loarca, Noah S Splinter, Bryce F Schutte, Nicholas F LaRusso
Primary sclerosing cholangitis (PSC) is a chronic, fibro-inflammatory cholangiopathy (disease of the bile ducts) of unknown pathogenesis. We reported that cholangiocyte senescence features prominently in PSC and neuroblastoma RAS viral oncogene homolog (NRAS) is activated in PSC cholangiocytes. Additionally, persistent microbial insult (e.g., lipopolysaccharides [LPS]) induces Cyclin Dependent Kinase Inhibitor 2A (CDKN2A/p16INK4a) expression and senescence in cultured cholangiocytes in an NRAS-dependent manner...
February 8, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28169281/gating-of-memory-encoding-of-time-delayed-cross-frequency-meg-networks-revealed-by-graph-filtration-based-on-persistent-homology
#7
Jarang Hahm, Hyekyoung Lee, Hyojin Park, Eunjoo Kang, Yu Kyeong Kim, Chun Kee Chung, Hyejin Kang, Dong Soo Lee
To explain gating of memory encoding, magnetoencephalography (MEG) was analyzed over multi-regional network of negative correlations between alpha band power during cue (cue-alpha) and gamma band power during item presentation (item-gamma) in Remember (R) and No-remember (NR) condition. Persistent homology with graph filtration on alpha-gamma correlation disclosed topological invariants to explain memory gating. Instruction compliance (R-hits minus NR-hits) was significantly related to negative coupling between the left superior occipital (cue-alpha) and the left dorsolateral superior frontal gyri (item-gamma) on permutation test, where the coupling was stronger in R than NR...
February 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28166814/closely-related-borrelia-burgdorferi-sensu-stricto-strains-exhibit-similar-fitness-in-single-infections-and-asymmetric-competition-in-multiple-infections
#8
Evelyn C Rynkiewicz, Julia Brown, Danielle M Tufts, Ching-I Huang, Helge Kampen, Stephen J Bent, Durland Fish, Maria A Diuk-Wasser
BACKGROUND: Wild hosts are commonly co-infected with complex, genetically diverse, pathogen communities. Competition is expected between genetically or ecologically similar pathogen strains which may influence patterns of coexistence. However, there is little data on how specific strains of these diverse pathogen species interact within the host and how this impacts pathogen persistence in nature. Ticks are the most common disease vector in temperate regions with Borrelia burgdorferi, the causative agent of Lyme disease, being the most common vector-borne pathogen in North America...
February 6, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28164792/characterization-and-function-of-mycobacterium-tuberculosis-h37rv-lipase-rv1076-lipu
#9
Chunyan Li, Qiming Li, Yuan Zhang, Zhen Gong, Sai Ren, Ping Li, Jianping Xie
Lipids and lipases/esterases are essential for Mycobacterium tuberculosis (Mtb) survival and persistence, even virulence. Mycobacterium tuberculosis H37Rv Rv1076 (LipU), a member of lipase family, is homologous to the human Hormone Sensitive Lipase (HSL) based on the presence of conserved motif 'GXSXG'. To define the enzymatic characteristics of rv1076, the gene was cloned, and expressed in Escherichia coli. The protein was purified for enzymatic characterization. LipU showed high specific activity for the hydrolysis of short carbon chain substrates with optimal activity at 40°C/pH 8...
March 2017: Microbiological Research
https://www.readbyqxmd.com/read/28161890/homology-guided-mutational-analysis-reveals-the-functional-requirements-for-antinociceptive-specificity-of-crmp2-derived-peptides
#10
Aubin Moutal, Wennan Li, Yue Wang, Weina Ju, Shizhen Luo, Song Cai, Liberty François-Moutal, Samantha Perez-Miller, Jackie Hu, Erik T Dustrude, Todd W Vanderah, Vijay Gokhale, May Khanna, Rajesh Khanna
BACKGROUND AND PURPOSE: N-type voltage-gated calcium (CaV2.2) channels are critical determinants of increased neuronal excitability and neurotransmission accompanying persistent neuropathic pain. Despite CaV2.2 antagonism being recommended as first-line treatment for neuropathic pain, calcium-current blocking gabapentinoids inadequately alleviate chronic pain symptoms and are often mired by numerous side-effects. Collapsin response mediator protein 2 (CRMP2) targets CaV2.2 to the sensory neuron membrane, and allosterically modulates Cav2...
February 5, 2017: British Journal of Pharmacology
https://www.readbyqxmd.com/read/28143524/homologous-prime-boost-immunization-with-live-attenuated-salmonella-enterica-serovar-senftenberg-and-its-preventive-efficacy-against-experimental-challenge-with-various-strains-of-s-senftenberg
#11
Nitin M Kamble, John Hwa Lee
BACKGROUND: The heterogeneity observed regarding persistence, and subsequent fecal shedding pattern of the Salmonella Senftenberg (S. Senftenberg) serovar in chicken's calls for development of the optimized immunization strategy which can provide protection against various S. Senftenberg isolated. Optimization of an immunization strategy with a live attenuated S. Senftenberg (Δlon and ΔcpxR) vaccine candidate (JOL1587) was undertaken in this study to evaluate the ability of a homologous prime-boost immunization strategy (using JOL1587) to confer protection against four different S...
January 31, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28141486/usefulness-of-humanized-cdna-upa-scid-mice-for-the-study-of-hepatitis-b-virus-and-hepatitis-c-virus-virology
#12
Takuro Uchida, Michio Imamura, Hiromi Kan, Nobuhiko Hiraga, C Nelson Hayes, Masataka Tsuge, Hiromi Abe-Chayama, Hiroshi Aikata, Grace Naswa Makokha, Daiki Miki, Hidenori Ochi, Yuji Ishida, Chise Tateno, Kazuaki Chayama
Urokinase-type plasminogen activator-severe combined immunodeficiency (uPA/SCID) mice transplanted with human hepatocytes are permissive for hepatitis B virus (HBV) and hepatitis C virus (HCV) infection. However, one of the problems affecting uPA transgenic mice is the expansion of mouse hepatocyte colonies due to homologous recombination of the uPA gene. In this study, we attempted to infect HBV and HCV in humanized cDNA-uPA/SCID mice, a novel uPA transgenic mouse model designed to overcome this disadvantage...
January 28, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28128333/comb-proteins-expression-levels-determine-helicobacter-pylori-competence-capacity
#13
Christopher Corbinais, Aurélie Mathieu, Prashant P Damke, Thierry Kortulewski, Didier Busso, Mariano Prado-Acosta, J Pablo Radicella, Stéphanie Marsin
Helicobacter pylori chronically colonises half of the world's human population and is the main cause of ulcers and gastric cancers. Its prevalence and the increase in antibiotic resistance observed recently reflect the high genetic adaptability of this pathogen. Together with high mutation rates and an efficient DNA recombination system, horizontal gene transfer through natural competence makes of H. pylori one of the most genetically diverse bacteria. We show here that transformation capacity is enhanced in strains defective for recN, extending previous work with other homologous recombination genes...
January 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28122581/acute-myeloid-leukemia-strategies-and-challenges-for-targeting-oncogenic-hedgehog-gli-signaling
#14
REVIEW
Fritz Aberger, Evelyn Hutterer, Christina Sternberg, Pedro J Del Burgo, Tanja N Hartmann
Treatment of acute myeloid leukemia (AML), an aggressive and heterogeneous hematological malignancy, remains a challenge. Despite advances in our understanding of the complex genetics and biology of AML pathophysiology, these findings have been translated to the clinic with only limited success, and poor outcomes persist for the majority of patients. Thus, novel treatment strategies are clearly needed for achieving deeper and prolonged remissions and for avoiding the development of resistance. Due to its profound role in (cancer) stem cell biology and differentiation, the Hedgehog (HH)/Glioma-associated Oncogene Homolog (GLI) signaling pathway may be an attractive novel therapeutic target in AML...
January 25, 2017: Cell Communication and Signaling: CCS
https://www.readbyqxmd.com/read/28100608/herpes-simplex-virus-type-1-ul24-abrogates-dna-sensing-signal-pathway-by-inhibiting-nf-%C3%AE%C2%BAb-activation
#15
Haiyan Xu, Chenhe Su, Angela Pearson, Christopher H Mody, Chunfu Zheng
: Cyclic GMP-AMP synthase (cGAS) is a newly identified DNA sensor that recognizes foreign DNA, including the genome of herpes simplex virus 1 (HSV-1). Upon binding of viral DNA, cGAS produces cyclic GMP-AMP, which interacts with and activates stimulator of interferon genes (STING) to trigger the transcription of anti-viral genes such as type I interferons and production of inflammatory cytokines. HSV-1 UL24 is widely conserved among the herpesviruses family and is essential for efficient viral replication...
January 18, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28056965/phylogenetic-characterization-of-genes-encoding-for-viral-envelope-glycoprotein-orf5-and-nucleocapsid-protein-orf7-of-porcine-reproductive-respiratory-syndrome-virus-found-in-malaysia-in-2013-and-2014
#16
Seetha Jaganathan King, Peck Toung Ooi, Lai Yee Phang, Zeenathul Nazariah Binti Allaudin, Wei Hoong Loh, Chiou Yan Tee, Shiao Pau How, Lai Siong Yip, Pow Yoon Choo, Ban Keong Lim
BACKGROUND: Porcine reproductive and respiratory syndrome (PRRS) is one of the most expensive diseases of modern swine production & results in annual economic losses and cost the industry over 600 million USD in U.S. alone and billions of dollars worldwide. Two atypical PRRS cases were observed in 2013 and 2014 characterized by late-term abortion, fever and sudden increase in sow mortality which persisted for a prolonged period of time. METHODS: Lungs, lymph nodes and other samples were collected for disease investigation...
January 5, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28052350/eses-software-for-eulerian-solvent-excluded-surface
#17
Beibei Liu, Bao Wang, Rundong Zhao, Yiying Tong, Guo-Wei Wei
Solvent excluded surface (SES) is one of the most popular surface definitions in biophysics and molecular biology. In addition to its usage in biomolecular visualization, it has been widely used in implicit solvent models, in which SES is usually immersed in a Cartesian mesh. Therefore, it is important to construct SESs in the Eulerian representation for biophysical modeling and computation. This work describes a software package called Eulerian solvent excluded surface (ESES) for the generation of accurate SESs in Cartesian grids...
March 15, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28049740/resolvase-osgen1-mediates-dna-repair-by-homologous-recombination
#18
Chong Wang, James D Higgins, Yi He, Pingli Lu, Dabing Zhang, Wanqi Liang
Yen1/GEN1 are canonical Holliday junction resolvases that belong to the RAD2/XPG family. In eukaryotes, such as budding yeast, mice, worms, and humans, Yen1/GEN1 work together with Mus81-Mms4/MUS81-EME1 and Slx1-Slx4/SLX1-SLX4 in DNA repair by homologous recombination to maintain genome stability. In plants, the biological function of Yen1/GEN1 remains largely unclear. In this study, we characterized the loss of function mutants of OsGEN1 and OsSEND1, a pair of paralogs of Yen1/GEN1 in rice (Oryza sativa). We first investigated the role of OsGEN1 during meiosis and found a reduction in chiasma frequency by ∼6% in osgen1 mutants, compared to the wild type, suggesting a possible involvement of OsGEN1 in the formation of crossovers...
February 2017: Plant Physiology
https://www.readbyqxmd.com/read/28046127/structure-function-network-mapping-and-its-assessment-via-persistent-homology
#19
Hualou Liang, Hongbin Wang
Understanding the relationship between brain structure and function is a fundamental problem in network neuroscience. This work deals with the general method of structure-function mapping at the whole-brain level. We formulate the problem as a topological mapping of structure-function connectivity via matrix function, and find a stable solution by exploiting a regularization procedure to cope with large matrices. We introduce a novel measure of network similarity based on persistent homology for assessing the quality of the network mapping, which enables a detailed comparison of network topological changes across all possible thresholds, rather than just at a single, arbitrary threshold that may not be optimal...
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28046077/an-oxygen-sensing-two-component-system-in-the-burkholderia-cepacia-complex-regulates-biofilm-intracellular-invasion-and-pathogenicity
#20
Matthew M Schaefers, Tiffany L Liao, Nicole M Boisvert, Damien Roux, Deborah Yoder-Himes, Gregory P Priebe
Burkholderia dolosa is a member of the Burkholderia cepacia complex (BCC), which is a group of bacteria that cause chronic lung infection in patients with cystic fibrosis (CF) and can be associated with outbreaks carrying high morbidity and mortality. While investigating the genomic diversity of B. dolosa strains collected from an outbreak among CF patients, we previously identified fixL as a gene showing signs of strong positive selection. This gene has homology to fixL of the rhizobial FixL/FixJ two-component system...
January 2017: PLoS Pathogens
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